1 B.Sc.III Microbiology Syllabus 2012 (SEMESTER PATTERN) Solapur University Solapur 2 B.SC.III (MICROBIOLOGY) COURSE STRUCTURE: Paper No Title of the paper Theory Lectures Semester- V Paper IX Virology, Extremophiles and Bioinformatics Theory 40 L Paper X Industrial Microbiology Theory 40 L Paper XI Agricultural Microbiology Theory 40 L Paper XII Immunology Theory 40 L Semester- VI Paper XIII Microbial Genetics Theory 40 L Paper XIV Microbial Biochemistry Theory 40 L Paper XV Environmental Microbiology Theory 40 L Theory 40 L Practical I Practical 20 P Practical II Practical 20 P Practical III Practical 20 P Practical IV Practical 20 P Paper XVI Medical Microbiology Practical Courses Study Tour 3 SOLAPUR UNIVERSITY, SOLAPUR B.Sc.III MICROBIOLOY SYLLABUS Semester V Paper IX: Virology, Extremophiles and Bioinformatics Unit I Classification of Viruses A) Viral classification, LHT system and as per international committee B) Isolation, cultivation, purification and enumeration of viruses Unit II Reproduction of bacteriophages A) One step growth experiment B) Reproduction of ds DNA/ ss DNA / RNA bacteriophages C) Temperate phages and lysogeny of λ phages Unit III Animal Viruses A) Reproduction of Animal viruses: Adeno viruses and Influenza viruses B) Oncogenic Viruses- Types of cancer, Characteristics of cancerous cells, Types of Oncogenic viruses; DNA and RNA viruses, Hypotheses of Cancer: Somatic mutation, Viral gene and Defective immunity Unit IV Extremophiles: General characteristics and their role in respective extreme environmentsAcidophiles, Alkalophiles, Thermophiles, Psychrophiles, Barophiles, Osmophiles Unit V Bioinformatics A) Introduction to Bioinformatics. Use of bioinformatics in major research areas B) Major Bioinformatics Resources on Internet: National Centre for Biotechnology Information (NCBI) i.The knowledge of various databases and bioinformatics tools available at NCBI resource ii.The major content of the NCBI databases iii.Purpose and applications in life sciences C) Protein data bank (PDB) and Nucleic acid sequence database (GenBank) D) The Basic Local Alignment Search Tool (BLAST) References: 1. Bergey’s Manual of Determinative Bacteriology- Breed and Buchanan 2. General microbiology – Stanier 3. General microbiology – Pawar and Daginawala Vol I and II 4. Genetics of bacteria and their viruses – William Hays 5. Virology – Biswas 6. Introduction of Bioinformatics – Affwood, T.K. 7. Bioinformatics by Shalini Suri 8. Virology – Luria 9. Physiology and Biochemistry of Extremophiles by Charles Gerday and Nicolas Glansdorff (2007) 10. http://www.ncbi.nlm.nih.gov/ 11. Prescutt, Harley and Klein’s Microbiology, Willey Sherwood Woolverton, McGraw – Hill International Edition, (2008) (8) (8) (8) (8) (8) 4 Paper X: Industrial Microbiology Unit I Food and dairy Microbiology A) Food as a substrate for microorganisms B) Food Fermentations – i) Idli ii) Bread C) Fermented dairy products: i) Cheese ii) curd iii) Yogurt Unit II Industrial Microbiology Industrial production of Alcoholic beverages A) Grape wine – Definition, types, production of White table wine, Red table wine, Sparkling wines - Champagne, California sherry, Post fermentation spoilage of wines: Microbial and non microbial spoilage of wines, Defects in wine B) Beer – Definition, types, production of Lager beer and Ales Beer. Unit III Industrial production of A) Streptomycin B) Lysine C) Biopolymers: Glucans and Dextrans D) rDNA products – Insulin, Interferon Unit IV Quality control in fermentation industry: A) Test for sterility, pyrogenicity, allergy, carcinogenicity, toxicity for Pharmaceutical and health care and food products B) Downstream processing: Filtration, Cross flow filtration, Flocculation, Whole broth processing Solvent extraction, Concentration, Centrifugation, Crystallization, Distillation, Adsorption elution, Precipitation and Chromatography Unit V Recent trends in fermentation Industry A) Good manufacturing practices in fermentation industry B) Computer applications in fermentation technology C) Fermentation economics References 1. Principles of fermentation technology – Stanbury and Whitekar 2. Dairy Technology – Sukumar De 3. Pharmaceutical Microbiology – Huggo and 4. Biochemistry – Fox and Nelson 5. Industrial Microbiology – Prescott and Dunn 6. Microbial technology – Peppler 7. Food Microbiology – R.C. Dubey, D.K. Mahashwari 8. Advances in Biotechnology – S.W. Jogdand. 9. Textbook of Biotechnology – R.C. Dubey, 10. Biotechnology – B.D. Singh 11. Industrial Microbiology – Casida 12. Industrial Microbiology – Patel A.H. (6) (08) (10) (10) (06) 5 Paper XI: Agricultural Microbiology Unit I Soil Microbiology A) Introduction - Definition, approaches to soil microbiology, current topics in soil microbiology B) Soil as an ecosystem C) Soil formation, structure and properties D) Soil microorganisms, types and their role (6) Unit II Role of microorganisms in A) Carbon cycle B) Nitrogen cycle C) Sulphur cycle D) Phosphorous cycle (8) Unit III Composting: Compost production with reference to organic waste, availability of microorganisms, aeration, C:N:P ratio, moisture control, temperature, pH and time a) Green manure b) Farm yard manure c) Town compost d) Vermicompost B) Biodegradation of Cellulose, Lignin, Pesticides and Hydrocarbons (10) Unit IV Plant pathology A) Common symptoms produced by plant pathogens B) Modes of transmission of Plant diseases: Oily spots on pomegranate – Xanthomonas aoxynopodis, white smut of sugarcane, soft rot of potato C) Control measures of plant diseases (8) Unit V Applications of Biotechnology in Agriculture References 1. Soil Microbiology – Subbarao, N.S. 2. Microbial dynamics and diversity – Desy Staley 3. Biology of Microorganisms – Brock, Parker, Madigen, 9th edition 4. Agricultural Microbiology- Bagyaraj and Ghosh 5. Plant Diseases- Singh R.S. 6. Soil Microbiology – Alexander. (4) 6 Paper XII: Immunology Unit I Complement system A) Components of complement and their properties, B) Activation of complement –classical and alternate pathway C) Biological effects of complement 4 Unit II Major Histocompatibility complex A) Organization of MHC genes in man Classes of MHC molecules – structure and their role B) Adaptive immunology a) Humoral (antibody) mediated response –Cells involved and mechanism b) Cell mediated – cells involved, mechanism; cytokines and their role UnitIII A) Monoclonal antibodies – i) Production (hybridoma technology) ii) Applications of Monoclonal antibodies in Diagnosis, Research and Treatment B) Basis of antibody diversity: Basic concept of Immunoglobulin gene, structure and its expression Unit IV A) Immunological tolerance B) Autoimmunity : i) Mechanism ii) Classification of Autoimmune diseases- a) Hemocytolytic b) Organ specific(Hashimotos disease, Graves disease, Myasthenia gravis, Pernicious anemia) c) Non organ specific(S.L.E., R.A.) C) Hypersensitivity : a) Introduction b) Types: i) Based on time required for manifestation-Immediate and delayed. ii)Based on pathogenesis ( TypeI:Anaphylaxis,Atopy; Type II, TypeIII:Arthus reaction, Serum sickness, Type IV:Delayed) D) Transplantation Immunology i) Terminologies ii) Classes of Transplants iii) Mechanisms of graft rejection iv) Prevention of graft Rejection v) HLA typing Unit V Immunohematology: A) ABO blood group system B) Rh blood group system C) Blood transfusion reaction and its complications D) Immunoprophalaxis – Conventional and new generation vaccines References 1. Essentials of Immunology Roitt Evan, Brostoff J. Male D. (1993) 6th Edition. 2. Immunology - Kuby J. (1996) - W.H. Freeman and Co. 3. Immunology – Fudenberg 4. Medical Microbiology - Davis and Dulbecco 5. Parasitology – Chattergii 6. Medical laboratory technology – Ramnaik Sood 7. Diagnostic Microbiology – Bailey’s and Scotts 8. Immunology – a problem approach by Wood, Hood and Weison 9. Medical Bacteriology – Dey and Dey 10. Handbook of Immunology- G.P. Talwar (1983) Vikas Publishing Pvt. Ltd 8 6 2 10 4 6 7 Semester VI Paper XIII: Microbial Genetics Unit I: Basic concepts of microbial genetics 8 A) Structural organization of Escherichia coli chromosome, folded fiber model B) Replication of DNA: Enzymes involved and mechanisms of replication C) Transcription: RNA polymerase enzyme, process and post transcriptional modification D) Operon concept – Lac Operon Unit II: Bacterial mutations A) Effect of mutation on translation B) Effect of mutation on phenotypes C) Time course of phenotypic expression D) Selection, detection & adaptation of mutants 8 Unit III: Genetic complementation A) Mutation in bacteriophages B) Cis-trans test 4 Unit IV: Genetic engineering and Protein engineering A) Introduction, Tools and Techniques of Genetic engineering B) Applications of Genetic engineering C) Protein Engineering – concept and applications 12 Unit V : Techniques in molecular biology A) Electrophoresis of DNA. B) DNA sequencing – Maxam and Gilbert’s method C) DNA finger printing- method and applications 8 References: 1. 2. 3. 4. 5. 6. 7. 9. General microbiology – Stanier General microbiology – Pawar and Daginawala Vol I and II Biochemistry – Lehninger Molecular Biology of Gene – J.D. Watson Recombinant DNA – J.D. Watson Microbiology - Davis Biochemistry - Purohit Genetics of bacteria and their viruses – William Hays 8 Paper XIV: Microbial Biochemistry Unit I Enzyme kinetics and regulation 10 A) Definition, properties, structure, specificity, mechanism of action (Lock and key model, induced fit hypothesis) B) Allosteric enzymes – Definition, Two models explaining mechanism of action (Sequential and Concerted) C) Ribosymes and Isozymes D) Factors affecting catalytic efficiency of enzymes i) Proximity, orientation ii) Strain and distortion iii) Acid base catalysis iv) Covalent catalysis E) Enzyme kinetics – Derivation of Michaelis Menten equation, Significance of Km and Vmax F) Regulation of enzyme synthesis i) Positive control – Arabinose Operon ii) End product repression – Tryptophan Operon iii) Catabolite repression Unit II Extraction, purification and assay of enzymes 6 A) Extraction, cell disruption and homogenization of membrane bound enzymes B) Purification of enzymes on the basis of differences in- i) Molecular size ii) Solubility iii) Electric charge iv) Adsorption characteristics) Biological affinity C) Immobilization of enzymes – Methods and applications D) Assay of enzymes (parameters: enzyme activity, Specific activity, turnover number, Bioassay) Unit III Assimilation of: i) Carbon ii) Nitrogen – N2 and NH3 (GOGAT) iii) Sulphur Unit IV Bioenergetics: A) Metabolic Pathways i) Glyoxylate bypass ii) PP Pathway iii) ED pathway iv) Phosphoketolase pathway v) Bioluminescence B) Pyruvate as key metabolite in Carbohydrate metabolism Unit V Biosynthesis of: A) Nucleotides B) Protein C) Peptidoglycan 6 8 10 9 References: 1. Biochemistry – Lehninger 2. Molecular Biology of Gene – J.D. Watson 3. Biochemistry - Purohit 4. Principles and techniques of Practical Biochemistry – K. Wilsons J.Walkar. 5. Analytical Chemistry – Robert B. Dilts 6. Chromatographic methods by Braithwaite and White 7. Outline of Biochemistry – Cohn and Stump 8. Biochemistry – West and Todd Russel 9. Biochemistry – Lehninger 10. Enzymes – Dixon and Web 11. Biological chemistry – Mahler and Cordes 12. Nature of Enzymology – R.L. Foster 13. Enzyme structure and Mechanism – Alen fereht 14. Biochemistry – Fox and Nelson 15. Microbial technology – Peppler 16. Biochemistry – A problem approach by Wood, Hood and Weison 10 Paper XV: Environmental Microbiology Unit I Air microbiology A) Microorganisms in air – Launching, transport and deposition of aerosols, survival of microorganisms in air B) Significance of microorganisms in air (extramural and intramural) C) Methods to study air borne microorganisms. Sampling, qualitative and quantitative methods. D) Bioaerosal control (ventilation, filtration, biocidal control, UV gaseous (quarantine) E) Sources, types, effects, control of air pollution. Depletion of ozone layer (causes, impact and control) F) Biological safety G) Germ free animal and Gnotobiology Unit II A) Marine microbiology Types of microorganisms in fresh and marine water, estuaries, methods to study aquatic microorganisms. Chracteristics of marine environment, types of organisms and their role. B) Eutrophication: a) Classification of lakes b) Sources C) Consequences d) Control Unit III Microbiology of potable water: Definition of potable water, Standard for potability, Municipal water purification process, Microorganisms as Bioindicators of fecal pollution, Routine bacteriological analysis of water. Unit IV Environmental impact assessment: A) Waste water assessment and management, types of wastes, chemical assessment, microflora, BOD, COD, treatment and disposal of waste water. B) Assessment and management of pollutants – toxic elements, their sources and effects and bioremediation (Lead, mercury, arsenic and radioactive substances) C) i) Environmental standards ii) Environmental legislations iii) Environmental education and awareness Unit V A) Bio-leaching: Introduction, Microorganisms involved, Biochemistry of microbial leaching, Commercial leaching – slope, heap, in situ leaching, Leaching of Copper and Uranium B) Oil recovery: Methods – primary, secondary, and microbially enhanced, Biotechnological solution of oil recovery C) Characteristics and treatment of wastes from different industries –paper and pulp, sugar and distillery, textile, and dairy industries D) Treatment of Biomedical waste 8 8 8 10 6 References: 1. Physiology and Biochemistry of Extremophiles- Charles Gerday and Nicolas Glansdorff 2. Environmental Microbiology – Maier 3. Microbial ecology – Fundamentals and applications - Atlas and Bartha 4. Microbial dynamics and diversity – Desy Staley 5. Biology of Microorganisms – Brock, Parker, Madigen, 9th edition 6. Microbiology – Prescott and Harley, 5th edition 11 Paper XVI: Medical Microbiology Unit I A) Pathogenicity of viruses, fungi and protozoa B) Hospital infection – factors contributing, common types, diagnosis and prophylaxis Unit II Bacterial diseases (Morphological, cultural and biochemical characters, antigenic structures, modes of transmission, pathogenesis, symptoms, laboratory diagnosis, prophylaxis and treatment of following diseases) 1. Pseudomonas aeruginosa 2. Mycobacterium leprae 3. Helicobacter pyelori 4. Treponema pallidum 5. Clostridium perfringens 6. Klebsiella pneumoniae 7. Vibrio cholerae Unit III Viral Diseases (Morphology, cultural and biochemical characters, antigenic structures, modes of transmission, pathogenesis, symptoms, laboratory diagnosis, prophylaxis and treatment of following diseases) 1. Herpes (Simplex) 2. Rabies 3. Hepatitis A and B 4. AIDS Unit IV Fungal, Protozoan Diseases and Biological Warfare a. Candidiasis b. Malaria (all four with comparative account) c. Biological warfare –Use of biological agents - bacteria, viruses, or other disease-causing agents as biological weapons Unit V Chemotherapy A) Antimicrobial Drugs B) Properties of ideal Antimicrobial drugs C) Mode of action of following antimicrobial drugs: i) Acting on Cell Wall: Penicillin, Bacitracin, Vancomycin, ii) Acting on Protein Synthesis: Streptomycin, Chloramphenicol, iii) Acting on nucleic acid synthesis: quinolenes, rifampicin iv) Drugs Acting on cell membrane: Sulphonamide, Trimethoprim, v) Antiviral drug: Azidothymidine, vi) Antifungal Drugs: Amphotericin, Nystatin D) Tests to guide chemotherapy a) diffusion tests b) broth dilution tests E) Mechanisms of drug resistance (4) (10) (10) (6) (10) 12 References: 1. Pharmaceutical Microbiology – Huggo 2. Text book of Medical Microbiology – Ananthnarayan 3. Review of Medical Microbiology – Jawetz et al 4. Microbiology – Zinsser 5. Medical Microbiology – Cruickshank 6. Medical Microbiology - Davis and Dulbecco 7. Parasitology – Chattergii 8. Medical laboratory technology – Ramnaik Sood 9. Diagnostic Microbiology – Bailey’s and Scotts 10. Medical Bacteriology – Dey and Dey 13 PRACTICAL COURSE Practical I: 1. Isolation of DNA from bacteria by J. Marmur’s method 2. Electrophoretic separation of DNA 3. Isolation of coliphages from sewage 4. One step growth curve 5. Determination of dose of U.V. by UV survival curve (comparative study of Escherichia coli and Staphylococcus aureus.) 7. Isolation of Lac negative mutants of E.coli by visual detection method. 8. Isolation of Streptomycin resistant mutants by gradient plate technique. 9. Isolation of Vitamin B12 requiring (auxotrophic) mutants by replica plate technique. 10. Diauxic growth curve of Escherichia coli (glucose and lactose). 11. Browsing of National Centre for Biotechnology Information (NCBI) website. 12. Exploring protein sequence database (PDB) and GenBank and BLAST. Practical II: 1. Examination of milk i) DMC ii) Quantitative analysis of milk by SPC (using nutrient agar) 2. Phosphatase Test (qualitative) 3. Bioassay of Vitamin B12 4. Bioassay of Penicillin 5. Production of wine by using Jaggery medium by S. cerevisiae - examination of pH, colour, taste. 6. Estimation of alcohol by using K2Cr2O7 7. Sterility testing of media 8. Immobilization of enzyme by using Sodium alginate 9. Thin layer chromatography- amino acid 10. Demonstration of crude recovery of amylase enzyme & Amylase assay 11. Isolation of Lactic acid Bacteria (MRS Medium) 12. Estimation of Citric acid by titration method 14 Practical III: 1. Isolation of Azotobacter from soil. (Identification up to genus level) 2. Isolation of Rhizobium from root nodules. 3. Isolation of Phosphate solubilising bacteria from soil. 4. Isolation of Xanthomonas from infected plant material 5. SPC of market Biofertilizers. 6. Estimation of available nitrogen from soil. 7. Estimation of available phosphorous from soil (Stannous chloride method) 8. Estimation of Calcium and Magnesium from soil (EDTA method) 9. Determination of organic carbon contents of soil (Walkley and Black method) 10. Microbiological analysis Drinking water: Presumptive, Confirmed and Completed test. 11. Determination of potability of water by MPN. 12. Waste water analysis: Chemical Oxygen Demand (COD), Biological Oxygen Demand (BOD) Practical IV: 1. Preparation of Tri sugar iron agar (TSI) medium slants and study of biochemical reactions on (TSI) slant. 2. Determination of minimum inhibitory concentration (MIC).of penicillin on S.aureus. 3. Antibiotic sensitivity test (by disc diffusion method) 4. Study of determination of effectiveness of antiseptic agents (– tincture iodine, 3% H2O2, 70% alcohol, 5% chlorine bleach) against selected organisms (Escherichia coli, Staphylococcus aureus, Bacillus) by disc diffusion method 5. A. Isolation of pathogen from clinical sample a) Pseudomonas aeruginosa b) Klebsiella pneumoniae c) Corybebacterium diphtheria B.Isolation and identification of member of Enterobacteriaceae (Maximum Two) up to species level from biomedical waste (Gram staining, colony characterization, motility and biochemical tests – IMViC, H2S, oxidase, catalase, urea hydrolysis, gelatin hydrolysis, phenylalanine deaminase test, lysine decarboxylase test, sugar fermentation) 6. Widal test (quantitative test) 7. Haematology – RBC count, WBC count, differential WBC count, Erythrocyte sedimentation rate (ESR) , Hemoglobin estimation and demonstration of malarial parasite. 8. Urine analysis a) Microscopic examination – pus cells, RBc, bacteria, crystals. b) Chemical examination – glucose (benedict’s method, protein (acetic acid), bile salt (sulphur method) ketone bodies (Rothera’s test) 9. Immunodiffusion test. 10. Study of synergistic action of antibiotics 15 Practical Examination A) The practical examination will be conducted on four (4) consecutive days for not less than 6 hours on each day of the practical examination. B) Each candidate must produce a certificate from the Head of the Department in his/her college stating that he/she has completed in a satisfactory manner the practical course on the guidelines laid down from time to time by Academic council on the recommendation of Board of studies and has recorded his/her observations in the laboratory journal and written a report on each exercise performed. Every journal is to be checked and signed periodically by a member teaching staff and certified by the Head of the Department at the end of the year. Candidates are to produce their journal at the time of practical examination. Candidate has to visit two places of Microbiological interest (Pharmaceutical industry, Dairy, Research institutes etc) and submit the report of their visit at the time of examination. The report should be duly certified by the Head of the Department. Distribution of Marks for practical examination For practical I, II, III, IV each. 1) One major experiment: 20 marks 2) Two minor experiment: 10 marks each 3) Journal: 5 marks Total marks: Practical I: 45 Marks Practical II: 45 Marks Practical III: 45 Marks Practical IV: 45 Marks Tour Report : 20 Marks Total Marks: 200 Practical wise distribution of marks Practical – I A) Major Experiments: (20) i) Isolation of coli phages/ Mutants OR ii) Electrophoresis separation of DNA B) Minor experiments: (20) 1) Diauxic growth / one step growth curve / Isolation of chromosomal DNA 2) Minimum lethal dose of U.V. by survival curve /Browsing of data banks (NCBI/ EBI/DDBJ) Practical II A) Major Experiments: (20) i) Bioassay of Penicillin / Vitamin B12 OR ii) Amylase assay/OR iii) TLC of amino acids OR iv) SPC of milk. OR v) Isolation of Lactic acid bacteria B) Minor experiments: (20) 1) Direct microscopic count of milk / Phosphatase test (qualitative) 2) Immobilization of enzymes /Estimation of citric acid by titration/ alcohol by k2Cr2O7 16 Practical III A) Major Experiments: (20) i) Isolation& identification of Azotobacter/Rhizobium/Xanthomonas OR ii) BOD of sewage sample OR iii) Estimation of nitrogen from soil B) Minor experiments: (20) 1) COD of sewage sample OR Estimation of calcium/ Magnesium/ Organic carbon of soil. 2) Determination of MPN of given sample OR Confirmed and Completed test OR Isolation of phosphate Solubilizing bacteria Practical – IV A) Major Experiments: (20) i) Isolation and identification of: Pseudomonas aeruginosa/ Klebsiella pneumoniae OR ii) Isolation and identification of Enterobacteriaceae up to species level from biomedical waste (Gram staining, colony characterization, motility and biochemical tests – IMViC, H2S, oxidase, catalase, urea hydrolysis, gelatin hydrolysis, phenylalanine deaminase test, lysine decarboxylase test, sugar fermentation test) B) Minor experiments: (20) 1) Determination of Antibiotic sensitivity to common pathogens OR Determination of MIC of Penicillin for S.aureus OR Determination of effectiveness of Antiseptic agents 2) Widal Test OR Differential count of blood OR Microscopic Examination of urine sample OR Chemical Examination of Urine for glucose/ Protein/ bile salt/ Ketone bodies OR ESR of blood sample OR Hb estimation of blood sample 17 List of the Minimum equipments and related requirements for B.Sc – III 1) Replica plating units for genetics experiments: Two 2) Rotary shaker for fermentation experiments: One 3) Centrifuge (High speed): One 4) Hot plate: One 5) Hot air oven: One 6) Bacteriological incubator: One 7) Spectrophotometer: One 8) Research Microscope: one for each student 9) Haemocytometer: Two 10) Haemoglobinometer: Two 11) ESR stands and tubes: Two 12) Separate room for fine instruments of size 10’×15’ feet dimension 13) A separate culture room of at least 10’×10’ feet dimension 14) Electrophoresis assembly: One 15) Laminar air flow cabinet: One 16) Distillation assembly: One (Glass) 17) Reflux assembly: Four 18) Serological water bath: One 19) Colony counter: One 20) Refrigerator: One 21) TLC UNIT: One 22) Hand Refractometer 23) Computer with Internet facilities and printer: One 24) Micropipette: One 25) Anaerobic Jar: One 26) Heating Mantle: One 27) UV Chamber